On July 24, 2012, Prigioni signed a one-year contract with the New York Knicks for the rookie minimum.[4] At age 35, Prigioni became the oldest NBA rookie in history when he made his debut on November 2, 2012. He became the team's starting point guard for the last two months of the 2012–13 season, as well as for the playoffs. In Game 6 of the New York Knicks' first round playoff series against the Boston Celtics, Prigioni made 3 three-pointers in the first quarter. The Knicks won 88-80 to advance to the second round of the playoffs for the first time in 13 years.[5]

On August 3, 2015, Prigioni signed with the Los Angeles Clippers.[9] On January 13, 2016, he had a career-high eight steals against the Miami Heat, one shy of the franchise record held by his coach, Doc Rivers.[10] On April 8, 2016, he recorded a season-high 13 points, a career-high seven rebounds, and a season-high seven assists in a 102–99 overtime win over the Utah Jazz.[11]

On July 29, 2016, Prigioni signed with the Houston Rockets, returning to the franchise for a second stint.[12] However, he was later waived by the Rockets on October 24 after appearing in five preseason games.[13]